Merge branch 'master' into feature/10591_scarf_reconstruction

Conflicts:
	Code/Mantid/Framework/Kernel/inc/MantidKernel/InternetHelper.h
	Code/Mantid/Framework/Kernel/src/InternetHelper.cpp

Smallish conflicts after changes in inet helper, re #10591

Code/Mantid/Build/CMake/DarwinSetup.cmake

@@ -131,20 +131,30 @@ else()
  set ( CMAKE_OSX_ARCHITECTURES x86_64 )
  set ( CMAKE_OSX_DEPLOYMENT_TARGET 10.8 )
  # Follow symlinks so cmake copies the file
- set ( PYQT4_PATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
+ # PYQT4_PATH, SITEPACKAGES_PATH, OPENSSL_ROOT_DIR may be defined externally (cmake -D)
+ # it would be good do not overwrite them (important for the compilation with macports)
+ if (NOT PYQT4_PATH)
+  set ( PYQT4_PATH /usr/local/lib/python${PY_VER}/site-packages/PyQt4 )
+ endif(NOT PYQT4_PATH)
  execute_process(COMMAND readlink ${PYQT4_PATH}/Qt.so OUTPUT_VARIABLE PYQT4_SYMLINK_Qtso)
- string(FIND ${PYQT4_SYMLINK_Qtso} "Qt.so" STOPPOS)
- string(SUBSTRING ${PYQT4_SYMLINK_Qtso} 0 ${STOPPOS} PYQT4_SYMLINK)
+ string(FIND "${PYQT4_SYMLINK_Qtso}" "Qt.so" STOPPOS)
+ string(SUBSTRING "${PYQT4_SYMLINK_Qtso}" 0 ${STOPPOS} PYQT4_SYMLINK)
  set  ( PYQT4_PYTHONPATH ${PYQT4_PATH}/${PYQT4_SYMLINK} )
+ string(REGEX REPLACE "/$" "" PYQT4_PYTHONPATH "${PYQT4_PYTHONPATH}")
 
- set ( SITEPACKAGES_PATH /usr/local/lib/python${PY_VER}/site-packages )
+ if (NOT SITEPACKAGES_PATH)
+   set ( SITEPACKAGES_PATH /usr/local/lib/python${PY_VER}/site-packages )
+ endif(NOT SITEPACKAGES_PATH)
  execute_process(COMMAND readlink ${SITEPACKAGES_PATH}/sip.so OUTPUT_VARIABLE SITEPACKAGES_SYMLINK_sipso)
- string(FIND ${SITEPACKAGES_SYMLINK_sipso} "sip.so" STOPPOS)
- string(SUBSTRING ${SITEPACKAGES_SYMLINK_sipso} 0 ${STOPPOS} SITEPACKAGES_SYMLINK)
+ string(FIND "${SITEPACKAGES_SYMLINK_sipso}" "sip.so" STOPPOS)
+ string(SUBSTRING "${SITEPACKAGES_SYMLINK_sipso}" 0 ${STOPPOS} SITEPACKAGES_SYMLINK)
  set  ( SITEPACKAGES ${SITEPACKAGES_PATH}/${SITEPACKAGES_SYMLINK} )
+ string(REGEX REPLACE "/$" "" SITEPACKAGES "${SITEPACKAGES}")
 
  # use homebrew OpenSSL package
- set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
+ if (NOT OPENSSL_ROOT_DIR)
+   set ( OPENSSL_ROOT_DIR /usr/local/opt/openssl )
+ endif(NOT OPENSSL_ROOT_DIR)
 endif()
 
 # Python packages

Code/Mantid/Build/CMake/LinuxPackageScripts.cmake

@@ -22,6 +22,10 @@ endif()
 
 set ( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${LIB_DIR};${CMAKE_INSTALL_PREFIX}/${PLUGINS_DIR};${CMAKE_INSTALL_PREFIX}/${PVPLUGINS_DIR} )
 
+# Tell rpm that this package does not own /opt /usr/share/{applications,pixmaps}
+# Required for Fedora >= 18 and RHEL >= 7
+set ( CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /opt /usr/share/applications /usr/share/pixmaps )
+
 ###########################################################################
 # LD_PRELOAD TCMalloc
 ###########################################################################

Code/Mantid/Build/Jenkins/jenkins-slave.sh

@@ -0,0 +1,84 @@
+#!/bin/sh
+#####################################################################
+# Starts the Jenkins slave process if it is not already running.
+# It also downloads the slave.jar to /tmp if it does not already
+# exist.
+#
+# The settings at the top must be filled in for each slave.
+#####################################################################
+# Crontab setting should be something like
+# 0,30 * * * * /home/builder/jenkins-linode/jenkins-slave.sh nodename secret
+# or (on mac)
+# 0,30 * * * * /Users/builder/jenkins-linode/jenkins-slave.sh nodename secret
+#####################################################################
+# User configuration
+#####################################################################
+# Main url for Jenkins
+JENKINS_URL=http://builds.mantidproject.org
+# URL for proxy (if required)
+PROXY_HOST=${3}
+# Port for proxy (if required)
+PROXY_PORT=${4}
+# Name of the node as it appears on jenkins
+NODE_NAME=${1}
+# Copy the secret from the command line given at the above URL
+SECRET=${2}
+
+#####################################################################
+# Constants
+#####################################################################
+# URL of jnlp file for slave
+SLAVE_AGENT_URL="${JENKINS_URL}/computer/${NODE_NAME}/slave-agent.jnlp"
+# name of the slave jar - full path is determined later
+JAR_FILE=slave.jar
+
+#####################################################################
+# Script
+#####################################################################
+# exit if it is already running
+RUNNING=$(ps aux | grep java | grep ${JAR_FILE})
+if [ ! -z "${RUNNING}" ]; then
+  echo "Slave process is already running"
+  exit 0
+else
+  echo "Slave process is not running"
+fi
+
+# error out if there isn't a node name and secret
+if [ "$#" -lt 2 ]; then
+  echo "Usage: `basename ${0}` <NODE_NAME> <SECRET> [PROXY_HOST] [PROXY_PORT]"
+  exit -1
+fi
+
+# setup the proxy
+if [ ! -z "${PROXY_HOST}" ]; then
+  PROXY_ARGS="-Dhttp.proxyHost=${PROXY_HOST} -Dhttp.proxyPort=${PROXY_PORT}"
+  echo "using proxy ${PROXY_HOST} ${PROXY_PORT}"
+  # For curl
+  export http_proxy=http://$PROXY_HOST:$PROXY_PORT
+fi
+
+# find the jar file if it exists
+if [ -f ${HOME}/jenkins-linode/${JAR_FILE} ]; then
+  JAR_FILE=${HOME}/jenkins-linode/${JAR_FILE}
+elif [ -f ${HOME}/Jenkins/${JAR_FILE} ]; then
+  JAR_FILE=${HOME}/Jenkins/${JAR_FILE}
+else
+  JAR_FILE=/tmp/${JAR_FILE}
+  if [ ! -f ${JAR_FILE} ]; then
+    echo "Downloading slave jar file to ${JAR_FILE}"
+    if [ $(command -v curl) ]; then
+      echo "curl -o ${JAR_FILE} ${JENKINS_URL}/jnlpJars/slave.jar"
+      curl -o ${JAR_FILE} ${JENKINS_URL}/jnlpJars/slave.jar
+    else
+      echo "Need curl to download ${JENKINS_URL}/jnlpJars/slave.jar"
+      exit -1
+    fi
+  fi
+fi
+
+echo "starting ..."
+JAVA=`which java`
+JAVA_ARGS="${PROXY_ARGS} -jar ${JAR_FILE} -jnlpUrl ${SLAVE_AGENT_URL} -secret ${SECRET}"
+echo "${JAVA} ${JAVA_ARGS}"
+${JAVA} ${JAVA_ARGS}

Code/Mantid/Build/dev-packages/deb/mantid-developer/README

@@ -2,5 +2,5 @@ This directory contains the structure required to build the simple mantid-develo
 
 To build the package:
    * Switch to the directory containing this file
-   * Run "dpkg --build mantid-developer-1.2.3"
-   * A file called mantid-developer-1.2.3.deb will appear in the current directory.
+   * Run "dpkg --build mantid-developer-1.2.4"
+   * A file called mantid-developer-1.2.4.deb will appear in the current directory.

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.3/DEBIAN/control

@@ -3,7 +3,7 @@ Version: 1.2.3
 Section: main
 Priority: optional
 Architecture: all
-Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive, texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme
 Installed-Size: 0
 Maintainer: Mantid Project <mantid-help@mantidproject.org>
 Description: Installs all packages required for a Mantid developer

Code/Mantid/Build/dev-packages/deb/mantid-developer/mantid-developer-1.2.4/DEBIAN/control

@@ -0,0 +1,13 @@
+Package: mantid-developer
+Version: 1.2.4
+Section: main
+Priority: optional
+Architecture: all
+Depends: git, clang, cmake-qt-gui(>=2.8.12), qt4-qmake, qt4-dev-tools, libqt4-dbg, libpoco-dev(>=1.4.2), libboost-all-dev, libboost-dbg, libnexus0-dev, libgoogle-perftools-dev, libqwt5-qt4-dev, libqwtplot3d-qt4-dev, python-qt4-dev, libgsl0-dev, liboce-visualization-dev, libmuparser-dev, python-numpy, libssl-dev, libqscintilla2-dev, texlive,texlive-latex-extra, dvipng, libhdf4-dev, doxygen, python-sphinx, python-scipy, ipython-qtconsole (>=1.2.0), libhdf5-dev, libhdf4-dev, libpococrypto11-dbg, libpocodata11-dbg, libpocofoundation11-dbg, libpocomysql11-dbg, libpoconet11-dbg, libpoconetssl11-dbg, libpocoodbc11-dbg, libpocosqlite11-dbg, libpocoutil11-dbg, libpocoxml11-dbg, libpocozip11-dbg, python-qt4-dbg, qt4-default, ninja-build, libjsoncpp-dev, python-dateutil, python-sphinx-bootstrap-theme, graphviz
+Installed-Size: 0
+Maintainer: Mantid Project <mantid-help@mantidproject.org>
+Description: Installs all packages required for a Mantid developer
+ A metapackage which requires all the dependencies and tools that are 
+ required for Mantid development. It works for Ubuntu version 14.04, 14.10
+ Some packages (poco) must be newer than those in the Ubuntu repository. Please 
+ follow instructions at http://www.mantidproject.org/Mantid_Prerequisites#Repositories

Code/Mantid/Build/dev-packages/rpm/mantid-developer/mantid-developer.spec

@@ -1,5 +1,5 @@
 Name:           mantid-developer
-Version:        1.7
+Version:        1.9
 Release:        1%{?dist}
 Summary:        Meta Package to install dependencies for Mantid Development
 
@@ -64,6 +64,7 @@ Requires: scl-utils
 Requires: qt-devel
 Requires: qtwebkit-devel
 %endif
+Requires: graphviz
 
 BuildArch: noarch
 
@@ -86,6 +87,9 @@ required for Mantid development.
 %files
 
 %changelog
+* Thu Feb 12 2015 Harry Jeffery <henry.jeffery@stfc.ac.uk>
+- Added graphviz dependency
+
 * Wed Aug 13 2014 Peter Peterson <petersonpf@ornl.gov>
 - Merged all three distribution spec files into one
 

Code/Mantid/Framework/API/inc/MantidAPI/IPeak.h

@@ -7,6 +7,7 @@
 #include "MantidKernel/Matrix.h"
 #include "MantidKernel/V3D.h"
 #include "MantidKernel/PhysicalConstants.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 namespace API {
@@ -50,9 +51,9 @@ class MANTID_API_DLL IPeak {
   virtual bool findDetector() = 0;
 
   virtual void setQSampleFrame(Mantid::Kernel::V3D QSampleFrame,
-                               double detectorDistance = 1.0) = 0;
+                               boost::optional<double> detectorDistance) = 0;
   virtual void setQLabFrame(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) = 0;
+                            boost::optional<double> detectorDistance) = 0;
 
   virtual void setWavelength(double wavelength) = 0;
   virtual double getWavelength() const = 0;

Code/Mantid/Framework/API/inc/MantidAPI/IPeaksWorkspace.h

@@ -7,6 +7,7 @@
 #include "MantidAPI/ITableWorkspace.h"
 #include "MantidAPI/ExperimentInfo.h"
 #include "MantidKernel/SpecialCoordinateSystem.h"
+#include <boost/optional.hpp>
 
 namespace Mantid {
 
@@ -98,12 +99,20 @@ class MANTID_API_DLL IPeaksWorkspace : public ITableWorkspace,
 
   //---------------------------------------------------------------------------------------------
   /** Create an instance of a Peak
-   * @param QLabFrame :: Q of the center of the peak, in reciprocal space
-   * @param detectorDistance :: distance between the sample and the detector.
+   * @param QLabFrame :: Q of the center of the peak in the lab frame, in reciprocal space
+   * @param detectorDistance :: Optional distance between the sample and the detector. Calculated if not provided.
    * @return a pointer to a new Peak object.
    */
   virtual IPeak *createPeak(Mantid::Kernel::V3D QLabFrame,
-                            double detectorDistance = 1.0) const = 0;
+                            boost::optional<double> detectorDistance) const = 0;
+
+
+  /**
+   * Create an instance of a peak using a V3D
+   * @param HKL V3D
+   * @return a pointer to a new Peak object.
+   */
+  virtual IPeak *createPeakHKL(Mantid::Kernel::V3D HKL) const = 0;
 
   //---------------------------------------------------------------------------------------------
   /** Determine if the workspace has been integrated using a peaks integration

Code/Mantid/Framework/API/src/Algorithm.cpp

@@ -1164,7 +1164,7 @@ bool Algorithm::checkGroups() {
     // Workspace groups are NOT returned by IWP->getWorkspace() most of the time
     // because WorkspaceProperty is templated by <MatrixWorkspace>
     // and WorkspaceGroup does not subclass <MatrixWorkspace>
-    if (!wsGroup && !prop->value().empty()) {
+    if (!wsGroup && prop && !prop->value().empty()) {
       // So try to use the name in the AnalysisDataService
       try {
         wsGroup = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(

Code/Mantid/Framework/API/src/MultiDomainFunction.cpp

@@ -141,27 +141,32 @@ void MultiDomainFunction::functionDeriv(const FunctionDomain &domain,
     throw std::invalid_argument(
         "Non-CompositeDomain passed to MultiDomainFunction.");
   }
-  const CompositeDomain &cd = dynamic_cast<const CompositeDomain &>(domain);
-  // domain must not have less parts than m_maxIndex
-  if (cd.getNParts() < m_maxIndex) {
-    throw std::invalid_argument(
-        "CompositeDomain has too few parts (" +
-        boost::lexical_cast<std::string>(cd.getNParts()) +
-        ") for MultiDomainFunction (max index " +
-        boost::lexical_cast<std::string>(m_maxIndex) + ").");
-  }
 
-  countValueOffsets(cd);
-  // evaluate member functions derivatives
-  for (size_t iFun = 0; iFun < nFunctions(); ++iFun) {
-    // find the domains member function must be applied to
-    std::vector<size_t> domains;
-    getDomainIndices(iFun, cd.getNParts(), domains);
+  if (getAttribute("NumDeriv").asBool()) {
+    calNumericalDeriv(domain, jacobian);
+  } else {
+    const CompositeDomain &cd = dynamic_cast<const CompositeDomain &>(domain);
+    // domain must not have less parts than m_maxIndex
+    if (cd.getNParts() < m_maxIndex) {
+      throw std::invalid_argument(
+          "CompositeDomain has too few parts (" +
+          boost::lexical_cast<std::string>(cd.getNParts()) +
+          ") for MultiDomainFunction (max index " +
+          boost::lexical_cast<std::string>(m_maxIndex) + ").");
+    }
 
-    for (auto i = domains.begin(); i != domains.end(); ++i) {
-      const FunctionDomain &d = cd.getDomain(*i);
-      PartialJacobian J(&jacobian, m_valueOffsets[*i], paramOffset(iFun));
-      getFunction(iFun)->functionDeriv(d, J);
+    countValueOffsets(cd);
+    // evaluate member functions derivatives
+    for (size_t iFun = 0; iFun < nFunctions(); ++iFun) {
+      // find the domains member function must be applied to
+      std::vector<size_t> domains;
+      getDomainIndices(iFun, cd.getNParts(), domains);
+
+      for (auto i = domains.begin(); i != domains.end(); ++i) {
+        const FunctionDomain &d = cd.getDomain(*i);
+        PartialJacobian J(&jacobian, m_valueOffsets[*i], paramOffset(iFun));
+        getFunction(iFun)->functionDeriv(d, J);
+      }
     }
   }
 }

Code/Mantid/Framework/API/src/PropertyNexus.cpp

@@ -193,7 +193,9 @@ Property *loadProperty(::NeXus::File *file, const std::string &group) {
   file->closeData();
   file->closeGroup();
   // add units
-  retVal->setUnits(unitsStr);
+  if (retVal)
+    retVal->setUnits(unitsStr);
+
   return retVal;
 }
 

Code/Mantid/Framework/API/test/MockObjects.h

@@ -103,9 +103,9 @@ namespace
     MOCK_METHOD0(findDetector,
       bool());
     MOCK_METHOD2(setQSampleFrame,
-      void(Mantid::Kernel::V3D QSampleFrame, double detectorDistance));
+      void(Mantid::Kernel::V3D QSampleFrame, boost::optional<double> detectorDistance));
     MOCK_METHOD2(setQLabFrame,
-      void(Mantid::Kernel::V3D QLabFrame, double detectorDistance));
+      void(Mantid::Kernel::V3D QLabFrame, boost::optional<double> detectorDistance));
     MOCK_METHOD1(setWavelength,
       void(double wavelength));
     MOCK_CONST_METHOD0(getWavelength,